improve dump scripts

8 files changed, 96 insertions, 0 deletions

diff --git a/extra/sql_dumps/README.md b/extra/sql_dumps/README.md
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+
+## HOWTO: Ident Table Snapshots
+
+How to take a consistent (single transaction) snapshot of 
+
+This will take somewhere around 15-25 GB of disk space on the database server
+(under /tmp). It would probably be better to stream this transaction over a
+network connection (saving database disk I/O), but I can't figure out how to do
+that with plain SQL (multiple table dumps in a single session), so would need
+to be a custom client.
+
+    ./ident_table_snapshot.sh
+
+## HOWTO: Dump abstracts, release identifiers, file hashes, etc
+
+These are run as regular old commands, and can run across the network in a
+couple different ways. We might not want database ports open to the network
+(even cluster/VPN); on the other hand we could proabably do SSH port
+forwarding anyways.
+
+    # Locally, or client running on a remote machine
+    psql fatcat < dump_abstracts.sql | egrep -v ^BEGIN$ | egrep -v ^ROLLBACK$ | pv -l | gzip > abstracts.json.gz
+
+    # Run on database server, write to file on remote host
+    psql fatcat < dump_abstracts.sql | egrep -v ^BEGIN$ | egrep -v ^ROLLBACK$ | pv -l | gzip | ssh user@host 'cat > abstracts.json.gz'
+
diff --git a/extra/sql_dumps/abstracts.json.gz b/extra/sql_dumps/abstracts.json.gz
new file mode 100644
index 00000000..2b6e3dc2
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+++ b/extra/sql_dumps/abstracts.json.gz
diff --git a/extra/sql_dumps/dump_abstracts.sql b/extra/sql_dumps/dump_abstracts.sql
new file mode 100644
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+++ b/extra/sql_dumps/dump_abstracts.sql
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+
+BEGIN TRANSACTION ISOLATION LEVEL SERIALIZABLE READ ONLY DEFERRABLE;
+
+COPY (SELECT row_to_json(abstracts) FROM abstracts) TO STDOUT WITH NULL '';
+
+ROLLBACK;
diff --git a/extra/sql_dumps/dump_file_hashes.sql b/extra/sql_dumps/dump_file_hashes.sql
new file mode 100644
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+++ b/extra/sql_dumps/dump_file_hashes.sql
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+
+BEGIN TRANSACTION ISOLATION LEVEL SERIALIZABLE READ ONLY DEFERRABLE;
+
+COPY (SELECT file_ident.id, file_rev.id, file_rev.sha1, file_rev.sha256, file_rev.md5
+      FROM file_rev
+      INNER JOIN file_ident ON file_ident.rev_id = file_rev.id
+      WHERE file_ident.is_live = 't' AND file_ident.redirect_id IS NULL)
+    TO STDOUT
+    WITH NULL '';
+
+ROLLBACK;
diff --git a/extra/sql_dumps/dump_idents.sql b/extra/sql_dumps/dump_idents.sql
new file mode 100644
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+++ b/extra/sql_dumps/dump_idents.sql
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+
+BEGIN TRANSACTION ISOLATION LEVEL SERIALIZABLE READ ONLY DEFERRABLE;
+
+COPY (SELECT id FROM changelog ORDER BY id DESC LIMIT 1)                         TO '/tmp/fatcat_ident_latest_changelog.tsv'    WITH NULL '';
+COPY (SELECT id, rev_id, redirect_id FROM creator_ident      WHERE is_live=true) TO '/tmp/fatcat_ident_creators.tsv'            WITH NULL '';
+COPY (SELECT id, rev_id, redirect_id FROM container_ident    WHERE is_live=true) TO '/tmp/fatcat_ident_containers.tsv'          WITH NULL '';
+COPY (SELECT id, rev_id, redirect_id FROM file_ident         WHERE is_live=true) TO '/tmp/fatcat_ident_files.tsv'               WITH NULL '';
+COPY (SELECT id, rev_id, redirect_id FROM release_ident      WHERE is_live=true) TO '/tmp/fatcat_ident_releases.tsv'            WITH NULL '';
+COPY (SELECT id, rev_id, redirect_id FROM work_ident         WHERE is_live=true) TO '/tmp/fatcat_ident_works.tsv'               WITH NULL '';
+COPY (SELECT id, editgroup_id, timestamp FROM changelog)                         TO '/tmp/fatcat_ident_changelog.tsv'           WITH NULL '';
+
+ROLLBACK;
diff --git a/extra/sql_dumps/dump_release_extid.sql b/extra/sql_dumps/dump_release_extid.sql
new file mode 100644
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+++ b/extra/sql_dumps/dump_release_extid.sql
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+
+BEGIN TRANSACTION ISOLATION LEVEL SERIALIZABLE READ ONLY DEFERRABLE;
+
+COPY (SELECT release_ident.id, release_rev.id, release_rev.doi, release_rev.pmcid, release_rev.pmid,
+             release_rev.core_id, release_rev.wikidata_qid
+      FROM release_rev
+      INNER JOIN release_ident ON release_ident.rev_id = release_rev.id
+      WHERE release_ident.is_live = 't' AND release_ident.redirect_id IS NULL)
+    TO STDOUT
+    WITH NULL '';
+
+ROLLBACK;
diff --git a/extra/sql_dumps/ident_table_snapshot.sh b/extra/sql_dumps/ident_table_snapshot.sh
new file mode 100755
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--- /dev/null
+++ b/extra/sql_dumps/ident_table_snapshot.sh
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+#!/bin/bash
+
+set -e -u -o pipefail
+
+DATESLUG="`date +%Y-%m-%d.%H%M%S`"
+DATABASE="fatcat"
+
+echo "Running SQL..."
+psql fatcat < ./dump_idents.sql
+
+CHANGELOG_REV="`head -n1 /tmp/fatcat_ident_latest_changelog.tsv`"
+OUTFILE="fatcat_idents.$DATESLUG.r$CHANGELOG_REV.tar.xz"
+
+echo "Compressing..."
+tar -C /tmp -c --xz --verbose \
+    -f $OUTFILE \
+    fatcat_ident_latest_changelog.tsv \
+    fatcat_ident_containers.tsv \
+    fatcat_ident_creators.tsv \
+    fatcat_ident_files.tsv \
+    fatcat_ident_releases.tsv \
+    fatcat_ident_works.tsv
+
+echo "Done: $OUTFILE"
diff --git a/extra/sql_dumps/thing.txt b/extra/sql_dumps/thing.txt
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+++ b/extra/sql_dumps/thing.txt
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+BEGIN
+{"sha1":"1ba86bf8c2979a62d29b18b537e50b2b093be27e","content":"some long abstract in plain text"}
+{"sha1":"0da908ab584b5e445a06beb172e3fab8cb5169e3","content":"<jats>A longer, more correct abstract should in theory go here</jats>"}
+{"sha1":"bd864bf5c612e64473e6b724c1d8f5e53a56bb6e","content":"<jats:p>This brief meeting review summarizes the recommendations of NSF and NPGI funded bioinformaticians concerning the future requirements for plant bioinformatics systems and databases.</jats:p>"}
+ROLLBACK